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Yorodumi- PDB-3f80: (S)-2-amino-6-nitrohexanoic acid binds to human arginase I throug... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3f80 | ||||||
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Title | (S)-2-amino-6-nitrohexanoic acid binds to human arginase I through multiple nitro-metal coordination interactions in the binuclear manganese cluster. Resolution 1.60 A. | ||||||
Components | Arginase-1 | ||||||
Keywords | HYDROLASE / Nitronium group coordination / surface plasmon resonance / Alternative splicing / Arginine metabolism / Cytoplasm / Disease mutation / Manganese / Metal-binding / Phosphoprotein / Polymorphism / Urea cycle | ||||||
Function / homology | Function and homology information positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginase activity / arginine catabolic process to ornithine / urea cycle / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation ...positive regulation of neutrophil mediated killing of fungus / Urea cycle / negative regulation of T-helper 2 cell cytokine production / arginase / arginase activity / arginine catabolic process to ornithine / urea cycle / negative regulation of type II interferon-mediated signaling pathway / defense response to protozoan / negative regulation of activated T cell proliferation / arginine catabolic process / negative regulation of T cell proliferation / specific granule lumen / azurophil granule lumen / manganese ion binding / adaptive immune response / innate immune response / Neutrophil degranulation / extracellular space / extracellular region / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Di Costanzo, L. / Christianson, D.W. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2008 Title: (S)-2-Amino-6-nitrohexanoic Acid Binds to Human Arginase I through Multiple Nitro-Metal Coordination Interactions in the Binuclear Manganese Cluster. Authors: Zakharian, T.Y. / Di Costanzo, L. / Christianson, D.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3f80.cif.gz | 138.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3f80.ent.gz | 106.9 KB | Display | PDB format |
PDBx/mmJSON format | 3f80.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3f80_validation.pdf.gz | 455.3 KB | Display | wwPDB validaton report |
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Full document | 3f80_full_validation.pdf.gz | 468 KB | Display | |
Data in XML | 3f80_validation.xml.gz | 28.5 KB | Display | |
Data in CIF | 3f80_validation.cif.gz | 41.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f8/3f80 ftp://data.pdbj.org/pub/pdb/validation_reports/f8/3f80 | HTTPS FTP |
-Related structure data
Related structure data | 2zavS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 34779.879 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ARG1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05089, arginase #2: Chemical | ChemComp-MN / #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.61 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 23, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection twin | Operator: -h,-k,l / Fraction: 0.468 |
Reflection | Resolution: 1.6→50 Å / Num. all: 83380 / Num. obs: 83380 / % possible obs: 99.8 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 25.3 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 3.5 / Num. unique all: 8330 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2ZAV, mon. A Resolution: 1.6→50 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree: 0.217 / Rfactor Rwork: 0.213 |